Notebooks http://bactra.org/notebooks
Cosma's NotebooksenPhysical Principles and Biologyhttp://bactra.org/notebooks/2015/12/13#physical-biology
<blockquote>The construction of the universe is certainly very much easier to
explain than is that of a plant ...
<br>---Lichtenberg, <cite>Aphorisms</cite> J 4</blockquote>
I don't <em>exactly</em> mean biophysics in the usual sense (e.g. things like
looking at the physical properties of proteins, or the other parts of what used
to be <a href="molecular-biology.html">molecular biology</a>, before the
DNA-sequencers pre-empted that name), interesting though that is. It's more
like wondering how much of biology --- especially the Big Things, like
evolution --- can be more or less directly explained by physics, or how tightly
physics constrains
biology. <a href="physics-information-computation.html">Physics constrains
computation</a>, (e.g., Landauer's principle: erasing a bit produces \( kT
\ln{2} \) joules of waste heat) --- might it also constrain evolution in an
analogous way? How useful are the mathematical tools physicists have come to
know and love in understanding biology? And so on.
<P>One long-running speculation along this line is that evolution has something
or other to do with thermodynamics. It would be nice to think so, but I've
never encountered any argument to this effect which is even remotely
convincing; the most prominent one these days is that advanced by Brooks and
Wiley in their book <cite>Evolution as Entropy</cite>: they claim that
speciation and natural selection <em>are</em> instances of the increase of
entropy. Unfortunately, they know squat-all about thermodynamics and <a
href="stat-mech.html">statistical mechanics</a>, and some of their examples
lead me to think they don't really understand <a
href="probability.html">probability</a> either. --- That said, I'd be
willing to bet (in a very modest way) that some version of the thermodynamic
<em>formalism</em> would actually be useful in describing evolution.
<P>A nice symmetry to biologists who don't understand physics is physicists who
don't understand biology: these also usually claim a connection between
physics and evolution, only in the area of self-organized criticality and the
supposed drive to the "<a href="edge-of-chaos.html">edge of chaos</a>." This
involves less the active errors of people like Brooks and Wiley as sheer
impatience with biological reality: as I heard one of its advocates put it
memorably, "Details don't matter!" But of course they do. (My paper
will Bill Tozier, below, is devoted to this critique.)
<P>Pure mechanics seems to be much more successful at saying interesting things
about biology; but much of this, like the square-cube law, is very old (that in
fact goes back to Galileo). The work by James Brown (no relation), Geoff West
et al., explaining "quarter-power" scaling laws in physiology, also looks
reasonably solid (even though it's about circulatory systems).
<ul>Recommended:
<li>Martin Barrett and Elliott Sober, "When and Why Does Entropy
Increase?", pp. 230--255 in Steven Savitt, <cite>Time's Arrows Today: Recent
Physical and Philosophical Work on the Direction of Time</cite> (Cambridge
UP, 1995) [A very nice paper on arrows of time, considering both the 2nd law of
thermodynamics and what Fisher called the "Fundamental Theorem of Natural
Selection," which latter, unlike the 2nd law, almost never applies to real
populations]
<li>Lionel Harrison, <cite>The Kinetic Theory of Living Form</cite>
[Inspired by Thompson, but much more chemical in approach, and much more at the
cellular level]
<li><a href="darcy-thompson.html">D'Arcy Thompson</a>, <cite>On Growth
and Form</cite> [Physical constraints on the forms and development of
organisms, and speculations on just how much of their shapes can be directly
explained by physical forces. The edition edited by <a
href="j-t-bonner.html">John Tyler Bonner</a> has notes on how well Thompson's
speculations have stood up under further research]
<li>Geoffrey West, James H. Brown and Brian J. Enquist, "A
General Model for the Origin of Allometric Scaling Laws in Biology",
<cite>Science</cite> <strong>276</strong> (1997): 122--126 [<a href="http://www.santafe.edu/media/workingpapers/97-03-019.pdf">PDF preprint</a> as Santa Fe Institute Working Paper 97-03-019]
</ul>
<ul>Modesty forbids:
<li>Cosma Rohilla Shalizi and William A. Tozier, "A Simple Model of
the Evolution of Simple Models of Evolution",
<a href="http://arxiv.org/abs/adap-org/9910002">adap-org/9910002</a> [Rejected
by <cite>Theoretical Population Biology</cite> for insufficient decorum.]
</ul>
<ul>To read:
<li>Howard C. Berg, <cite><a href="http://press.princeton.edu/titles/112.html">Random Walks in Biology</a></cite>
<li>William Bialek
<ul>
<li>"Thinking about the brain,"
<a href="http://arxiv.org/abs/physics/0205030">physics/0205030</a>
<li><cite><a href="http://press.princeton.edu/titles/9911.html">Biophysics:
Searching for Principles</a></cite>
</ul>
<li>William Bialek and Sima Setayeshgar, "Physical limits to
biochemical signaling," <a
href="http://arxiv.org/abs/physics/0301001">physics/0301001</a> = <a
href="http://dx.doi.org/10.1073/pnas.0504321102"><cite>PNAS</cite> <strong>102</strong>
(2005): 10040--10045</a>
<li>James H. Brown and Geoffrey B. West (eds.), <cite>Scaling in Biology</cite>
<li>Michael Burton, "Ecosystems, from life, to the Earth, to the
Galaxy,"
<a href="http://arxiv.org/abs/astro-ph/0110694">astro-ph/0110694</a>
<li>William A. Calder III, <cite>Size, Function and Life History</cite>
<li>Pierre-Henri Chavanis, "Phase separation of bacterial colonies in a
limit of high degradation. Analogy with Jupiter's great red
spot", <a href="http://arxiv.org/abs/physics/0607020">physics/0607020</a>
<li>Peter Sheridan Dodds, "On the optimal form of branching supply and collection networks", <a href="http://arxiv.org/abs/0909.1104">arxiv:0909.1104</a>
<li>Sean Escola, Michael Eisele, Kenneth Miller and Liam
Paninski, "Maximally Reliable Markov Chains Under Energy Constraints",
<a href="http://dx.doi.org/10.1162/neco.2009.08-08-843"><cite>Neural Computation</cite>
<strong>21</strong> (2009): 1863--1912</a>
<li>Gabor Forgacs andStuart A. Newman, <cite><a href="http://cambridge.org/9780521783378">Biological Physics of
the Developing Embryo</a></cite>
<li>Joachim Hermisson, Oliver Redner, Holger Wagner and Ellen Baake,
"Mutation-Selection Balance: Ancestry, Load, and Maximum Principle,"
<a href="http://arxiv.org/abs/cond-mat/0202432">cond-mat/0202432</a>
<li>I. R. Kennedy, <cite>Action in Ecosystems: Biothermodynamics for
Sustainability</cite>
<li>Lotka, <cite>Elements of Physical Biology</cite> [Dover reprint as
<cite>Elements of Mathematical Biology</cite>]
<li>Karo Michaelian, "A Non-equilibrium Thermodynamic Framework for
the Dynamics and Stability of Ecosystems,"
<a href="http://arxiv.org/abs/physics/0204065">physics/0204065</a> [I really
want to read this, but the mere fact it's submitted to Phys. Rev. E, and
not, say, <cite>The Journal of Theoretical Biology</cite> makes me
skeptical.]
<li>N. Rashevsky, <cite>Mathematical Bio-Physics</cite>
<li>Glenn Rowe, <cite>Theoretical Models in Biology: The Origin of
Life, the Immune System and the Brain</cite>
<li>Schmidt-Nielsen, <cite>Scaling</cite>
<li>Guy Sella and Aaron E. Hirsh, "The application of statistical
physics to evolutionary biology", <a
href="http://dx.doi.org/10.1073/pnas.0501865102"><cite>Proceedings of the
National Academy of Sciences</cite> <strong>102</strong> (2005): 9541--9546</a>
<li>L. Sertorio and Giovanna Tinetti, "Available Energy for Life on a
Planet, with or without Stellar Radiation,"
<a href="http://arxiv.org/abs/astro-ph/0107313">astro-ph/0107313</a>
<li>Gasper Tkacik, "From statistical mechanics to information theory: understanding biophysical information-processing systems", <a href="http://arxiv.org/abs/1006.4291">arxiv:1006.4291</a>
<li>Erkan Tuzel and Ayse Erzan, "A Thermodynamic Model for Prebiotic
RNA-Protein Co-evolution,"
<a href="http://arxiv.org/abs/cond-mat/0107315">cond-mat/0107315</a>
<li>Erik van Nimwegen, <cite>The Statistical Dynamics of Epochal
Evolution</cite> [<a href="http://www.santafe/~erik/net_thesis.ps.gz">gzipped
PostScript</a>]
<li>Steven Vogel
<ul>
<li><cite>Comparative Biomechanics: Life's Physical World</cite>
<li><cite>Glimpses of Creatures in Their Physical
Worlds</cite>
</ul>
<li>Volkstein, <cite>Physical Approaches to Biological Evolution</cite>
<li>Muhammad H. Zaman (ed.), <cite><a href="http://cambridge.org/9780521886086">Statistical Mechanics of Cellular Systems and Processes</a></cite>
</ul>
<ul>To shoot after fair trials:
<li>P. Ao, "Mathematical Structure of Evolutionary Theory", <a
href="http://arxiv.org/abs/q-bio.QM/0403020">q-bio.QM/0403020</a> ["Here we
postulate three laws which form a mathematical framework to capture the essence
of Darwinian evolutionary dynamics. The second law is most quantitative and is
explicitly expressed by a unique form of stochastic differential equation."
Color me skeptical, but I haven't read beyond the abstract.]
<LI>Blum, <cite>Time's Arrow and Evolution</cite>
<li>Doriano Brogioli, "Marginally Stable Chemical Systems as Precursors
of
Life", <a href="http://dx.doi.org/10.1103/PhysRevLett.105.058102"><cite>Physical
Review Letters</cite>
<strong>105</strong> (2010): 058102</a>
<li>Debashish Chowdhury, Dietrich Stauffer and Ambarish Kunwar,
"Unification of Small and Large Time Scales for Biological Evolution:
Deviations from Power Law," <cite>Physical Review
Letters</cite> <strong>90</strong> (2003): 068101
<li>Siegfried Fussy, Gerhard Groessing and Herbert Schwabl, "A Simple
Model for the Evolution of Evolution,"
<a href="http://arxiv.org/abs/physics/0204070">physics/0204070</a> =
<cite>J. Biol. Systems</cite> <strong>5</strong> (1997): 341--357
<li>Pankaj Mehta and David J. Schwab, "Energetic costs of cellular computation", <a href="http://dx.doi.org/10.1073/pnas.1207814109"><cite>Proceedings of the National Academy of Sciences</cite>(USA) <strong>109</strong> (2012):
17978--17982</a>
<li>Thierry Mora, William Bialek, "Are biological systems poised at criticality?", <a href="http://arxiv.org/abs/1012.2242">arxiv:1012.2242</a>
<li>Per Arne Rikvold and R. K. P. Zia, "Flicker Noise in a Model of
Coevolving Biological Populations," <a
href="http://arxiv.org/abs/nlin.AO/0303010">nlin.AO/0303010</a>
<li>Hideaki Shimazaki and Ernst Niebur, "Bose-Einstein Condensation and
the Principles of Competitive Process," <a
href="http://arxiv.org/abs/cond-mat/0303298">cond-mat/0303298</a> [Sounds like
a convoluted rediscovery of the replicator equation]
<li>Weber, Depew and Smith (eds.), <cite>Entropy, Information, and
Evolution: New Perspectives on Physical and Biological Evolution</cite>
<li>Jeffrey Wicken, <cite>Evolution, Thermodynamics and Information:
Extending the Darwinian Program</cite>
</ul>